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Sample GSM252344 Query DataSets for GSM252344
Status Public on Dec 01, 2008
Title Human Prostate 650
Sample type RNA
 
Channel 1
Source name Reference
Organism Homo sapiens
Characteristics Reference
Extracted molecule total RNA
Extraction protocol Prostate samples embedded in OCT were used for laser capture microdissection (LCM) by the laboratory of Martin Gleave. Total RNA was isolated from microdissected cells using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.
Label Cy5
Label protocol Complementary DNA (cDNA) probe pairs were prepared by amino-allyl reverse transcription using 2 µg of amplified RNA from microdissected samples and 30 µg of total RNA from a reference RNA pool composed of total RNA isolated from the LNCap, DU145, and PC3 prostate cell lines. Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
 
Channel 2
Source name Human Prostate 650 treated with Neoadjuvant hormone suppression for 6 mo
Organism Homo sapiens
Characteristics Human Prostate 650. #: 650; Treatment: Neoadjuvant hormone suppression for 6 mo; Reference: HGSv5;
Extracted molecule total RNA
Extraction protocol Prostate samples embedded in OCT were used for laser capture microdissection (LCM) by the laboratory of Martin Gleave. Total RNA was isolated from microdissected cells using the Arcturus Picopure™ Kit, and the samples were treated with DNAse using the Qiagen RNase-Free DNase Set (Qiagen Inc, Valencia, CA). Total RNA was subjected to two rounds of linear amplification using the Ambion MessageAmpII Kit (Ambion Inc, Austin, TX), quantitated in a Gene-Spec III spectrophotometer (Hitachi, Tokyo) and aRNA integrity evaluated using gel electrophoresis.
Label Cy3
Label protocol Complementary DNA (cDNA) probe pairs were prepared by amino-allyl reverse transcription using 2 µg of amplified RNA from microdissected samples and 30 µg of total RNA from a reference RNA pool composed of total RNA isolated from the LNCap, DU145, and PC3 prostate cell lines. Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
 
 
Hybridization protocol Probes were labeled with either Cy5 or Cy3 fluors (Amersham Bioscience, Piscataway, NJ) and competitively hybridized to custom cDNA microarrays spotted in duplicate with approximately 6,700 unique cDNA clones from the Prostate Expression Database (PEDB) as previously described in Nelson PS, Pritchard C, Abbott D, and Clegg N. The human (PEDB) and mouse (mPEDB) Prostate Expression Databases. Nucleic Acids Res 2002;30:218-220 and Pritchard CC, Hsu L, Delrow J, and Nelson PS. Project normal: defining normal variance in mouse gene expression. Proc Natl Acad Sci U S A 2001;98:13266-13271.
Scan protocol Fluorescence array images were collected using a GenePix 4000B fluorescent scanner (Axon Instruments, Foster City, CA) and processed as we have previously described in True L, Coleman I, Hawley S, et al. A molecular correlate to the Gleason grading system for prostate adenocarcinoma. Proc Natl Acad Sci U S A 2006;103:10991-10996.
Description Human Prostate 650 from Human hybridized against Reference
Data processing Changes in gene expression were evaluated using the Statistical Analysis of Microarray (SAM) program (http://www-stat.stanford.edu/_tibs/SAM/) to perform a one-sample t-test assessing the effect of Acyline treatment on gene expression (22). An FDR (false discovery rate) of less than 5% was considered significant. Quantile normalization was performed in Bioconductor (23) to allow single channel comparison of the absolute signal intensities in the experimental channel across different arrays in the same experiment.
 
Submission date Dec 19, 2007
Last update date Dec 28, 2007
Contact name Denise Mauldin
E-mail(s) [email protected]
Phone 2066673480
Fax 2066672917
URL http://www.pedb.org
Organization name Fred Hutchinson Cancer Research Center
Department Human Biology
Lab Peter Nelson
Street address 1100 Fairview Ave N D4-100
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL4768
Series (1)
GSE9983 Prostate Cancer Gene Expression Changes with Neoadjuvant Hormone Therapy

Data table header descriptions
ID_REF the unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks).
VALUE normalized log (experiment/reference) ratio data comparable across rows and samples
MetaCol Column referring to overall organization
MetaRow Row referring to overall organization
Column the column number of the feature.
Row the row number of the feature.
Name the name of the feature derived from the Array List (up to 40 characters long, contained in quotation marks).
X the X-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y the Y-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Dia. the diameter in µm of the feature-indicator.
F635 Median median feature pixel intensity at wavelength #1 (635 nm).
F635 Mean mean feature pixel intensity at wavelength #1 (635 nm).
F635 SD the standard deviation of the feature pixel intensity at wavelength #1 (635 nm).
F635 CV the coefficient of variation of feature pixel intensity.
B635 the actual background value used for the feature in GenePix Pro calculations (as opposed to B635 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B635 is different to B635 Median
B635 Median the median feature background intensity at wavelength #1 (635 nm).
B635 Mean the mean feature background intensity at wavelength #1 (635 nm).
B635 SD the standard deviation of the feature background intensity at wavelength #1 (635 nm).
B635 CV the coefficient of variation of background pixel intensity.
% > B635+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm).
% > B635+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. the percentage of feature pixels at wavelength 635 that are saturated.
F532 Median median feature pixel intensity at wavelength #2 (532 nm).
F532 Mean mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD the standard deviation of the feature intensity at wavelength #2 (532 nm).
F532 CV the coefficient of variation of feature pixel intensity.
B532 the actual background value used for the feature in GenePix Pro calculations (as opposed to B532 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B532 is different to B532 Median.
B532 Median the median feature background intensity at wavelength #2 (532 nm).
B532 Mean the mean feature background intensity at wavelength #2 (532 nm).
B532 SD the standard deviation of the feature background intensity at wavelength #2 (532 nm).
B532 CV the coefficient of variation of background pixel intensity.
% > B532+1SD the percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm).
% > B532+2SD the percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm).
F532 % Sat. the percentage of feature pixels at wavelength 532 that are saturated.
Ratio of Medians (635/532) the ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Ratio of Means (635/532) the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios (635/532) the median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios (635/532) the geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD (635/532) the geometric standard deviation of the pixel intensity ratios.
Rgn Ratio (635/532) the regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R2 (635/532) the coefficient of determination for the current regression value.
F Pixels the total number of feature pixels.
B Pixels the total number of background pixels.
Circularity a measure of circularity from 0 to 100, using a metric based on the variance of the distance of each boundary pixel to the centroid of the feature: 100 is most circular, 0 is most non-circular. Circular features always have a circularity of 100, square features always have a circularity of 79 (
Sum of Medians (635/532) the sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means (635/532) the sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Log Ratio (635/532) log (base 2) transform of the ratio of the medians.
F635 Median - B635 the median feature pixel intensity at 635 with the median background subtracted.
F532 Median - B532 the median feature pixel intensity at 532 with the median background subtracted.
F635 Mean - B635 the mean feature pixel intensity at 635 with the median background subtracted.
F532 Mean - B532 the mean feature pixel intensity at 532 with the median background subtracted.
F635 Total Intensity the sum of all pixel intensities in the feature at wavelenth 635.
F532 Total Intensity the sum of all pixel intensities in the feature at wavelenth 532.
SNR 635 the signal-to-noise ratio of the feature, calculated as (F635 Mean - B635 Mean)/B635 SD.
SNR 532 the signal-to-noise ratio of the feature, calculated as (F532 Mean - B532 Mean)/B532 SD.
Flags the type of flag associated with a feature.
Normalize the normalization status of the feature (included/not included).
Autoflag reports whether or not a feature has been flagged from the Flag Features dialog box. It applies to good and bad flags only.

Data table
ID_REF VALUE MetaCol MetaRow Column Row Name X Y Dia. F635 Median F635 Mean F635 SD F635 CV B635 B635 Median B635 Mean B635 SD B635 CV % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532 B532 Median B532 Mean B532 SD B532 CV % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R2 (635/532) F Pixels B Pixels Circularity Sum of Medians (635/532) Sum of Means (635/532) Log Ratio (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags Normalize Autoflag
237241 0.239037842 1 1 1 1 gi|220150|gb|D90427|D90427 2700 9560 140 2431 2437 518 21 458 458 469 122 26 100 100 0 1954 2069 667 32 298 298 302 68 22 100 100 0 1.191 1.117 1.142 1.144 1.417 1.043 0.779 156 820 100 3629 3750 0.253 1973 1656 1979 1771 380139 322719 16.131 25.985 0 0 0
237242 -4.494572563 1 1 2 1 gi|179280|gb|M27132.1|HUMATPSYB 2880 9550 130 23695 25358 10698 42 472 472 480 97 20 100 100 0 2689 2629 978 37 303 303 306 59 19 100 100 0 9.733 10.699 10.988 10.915 1.381 11.115 0.915 120 635 100 25609 27212 3.283 23223 2386 24886 2326 3042950 315519 256.474 39.373 0 0 0
237243 1 1 3 1 gi|12420723|gb|BG030944|BG030944 3080 9550 140 469 481 90 18 474 474 486 120 24 11 1 0 306 309 68 22 305 305 319 175 54 1 0 0 -5.000 1.750 1.397 1.385 4.397 20.538 0.001 156 760 100 -4 11 Error -5 1 7 4 74984 48129 -0.042 -0.057 -50 0 0
237244 -0.771208886 1 1 4 1 gi|21536438|ref|NM_012161.2| 3280 9550 120 2692 2553 769 30 476 476 479 92 19 100 100 0 1071 1045 366 35 303 303 306 63 20 96 93 0 2.885 2.799 2.824 3.084 1.627 2.782 0.843 120 560 100 2984 2819 1.529 2216 768 2077 742 306394 125365 22.543 11.730 0 0 0
237245 -0.615912164 1 1 5 1 gi|21536438|ref|NM_012161.2| 3470 9560 120 2600 2468 761 30 474 474 478 93 19 100 100 0 1165 1121 307 27 300 300 305 62 20 100 99 0 2.458 2.429 2.435 2.440 1.463 2.545 0.876 120 545 100 2991 2815 1.297 2126 865 1994 821 296183 134472 21.398 13.161 0 0 0
237246 1 1 6 1 gi|14065685|gb|BG755019|BG755019 3660 9540 140 442 444 90 20 455 455 461 90 19 10 1 0 290 298 102 34 298 298 303 67 22 7 1 0 1.625 100000.000 1.688 1.641 4.664 3.296 0.009 156 759 100 -21 -11 0.700 -13 -8 -11 0 69297 46516 -0.189 -0.075 -50 0 0
237247 1 1 7 1 gi|15996756|gb|BI856009|BI856009 3860 9540 140 455 456 87 19 453 453 459 109 23 12 0 0 287 292 61 20 297 297 301 60 19 10 3 0 -0.200 -0.600 2.152 2.007 3.817 22.680 0.001 156 717 100 -8 -2 Error 2 -10 3 -5 71101 45621 -0.028 -0.150 -50 0 0
237248 1 1 8 1 gi|19586973|gb|BM969386|BM969386 4050 9540 140 465 477 98 20 458 458 469 124 26 14 1 0 307 310 64 20 300 300 305 61 20 16 5 0 1.000 1.900 1.591 1.867 4.425 14.060 0.000 156 733 100 14 29 0.000 7 7 19 10 74388 48353 0.065 0.082 -50 0 0
237249 -3.510186965 1 1 9 1 gi|7703647|gb|AW771590| 4250 9540 110 20907 22671 8639 38 477 477 499 171 34 100 100 0 3971 4054 1340 33 308 308 320 86 26 100 100 0 5.577 5.925 5.726 5.948 1.418 6.303 0.893 80 478 100 24093 25940 2.480 20430 3663 22194 3746 1813647 324281 129.661 43.419 0 0 0
237250 1 1 10 1 gi|20408448|gb|BQ227048|BQ227048 4440 9540 140 445 457 87 19 489 489 501 145 28 1 0 0 304 306 58 18 311 311 320 80 25 10 0 0 6.286 6.400 1.474 1.583 5.418 5.345 0.068 156 763 100 -51 -37 2.652 -44 -7 -32 -5 71232 47678 -0.303 -0.175 -50 0 0
237251 -1.496088993 1 1 11 1 gi|11012215|gb|AU150694|AU150694 4620 9540 130 3324 3279 831 25 485 485 491 90 18 100 100 0 933 967 280 28 315 315 320 71 22 99 99 0 4.594 4.285 4.311 4.549 1.637 4.475 0.738 120 625 100 3457 3446 2.200 2839 618 2794 652 393454 116075 30.978 9.113 0 0 0
237252 1 1 12 1 gi|17298590|gb|AC009167.8| 4830 9530 140 480 489 88 17 480 480 487 89 18 17 5 0 294 305 75 24 308 308 318 166 52 2 0 0 0.000 -3.000 1.491 1.376 4.280 42.834 0.000 156 749 100 -14 6 Error 0 -14 9 -3 76313 47615 0.022 -0.078 -50 0 0
237253 -0.926192816 1 1 13 1 gi|13477360|gb|BC005157|BC005157 5000 9530 130 1874 1890 448 23 485 485 492 93 18 100 100 0 938 947 221 23 305 305 318 180 56 97 90 0 2.194 2.188 2.105 2.263 1.703 2.160 0.524 120 621 100 2022 2047 1.134 1389 633 1405 642 226791 113625 15.032 3.494 0 0 0
237254 1 1 14 1 UNKNOWN_4 5220 9530 140 490 492 95 19 486 486 494 103 20 14 3 0 300 304 62 20 302 302 309 60 19 16 3 0 -2.000 3.000 1.371 1.229 4.387 15.212 0.002 156 732 100 2 8 Error 4 -2 6 2 76695 47353 -0.019 -0.083 -50 0 0
237255 1 1 15 1 gi|5031976|ref|NM_005746.1| 5410 9530 140 490 501 91 18 484 484 496 100 20 19 2 0 312 315 66 20 299 299 306 60 19 22 7 0 0.462 1.063 1.303 1.357 4.302 29.505 0.001 156 662 100 19 33 -1.115 6 13 17 16 78159 49128 0.050 0.150 -50 0 0
237256 1 1 16 1 gi|4827043|ref|NM_005121.1| 5600 9530 140 508 512 104 20 497 497 501 94 18 21 5 0 312 318 68 21 300 300 307 62 20 20 4 0 0.917 0.833 1.545 1.863 5.546 5.566 0.021 156 711 100 23 33 -0.126 11 12 15 18 79937 49644 0.117 0.177 -50 0 0
237257 1 1 17 1 BLANK 5800 9520 140 515 552 310 56 496 496 501 91 18 24 5 0 319 335 97 28 304 304 309 63 20 22 8 0 1.267 1.806 1.585 1.439 4.918 7.607 0.073 156 738 100 34 87 0.341 19 15 56 31 86127 52331 0.560 0.413 -50 0 0
237258 1 1 18 1 UNKNOWN_6 5990 9520 140 529 527 135 25 499 499 505 95 18 19 3 0 315 318 64 20 305 305 312 70 22 14 3 0 3.000 2.154 1.777 1.453 3.615 5.426 0.036 156 720 100 40 41 1.585 30 10 28 13 82143 49609 0.232 0.086 -50 0 0
237259 -0.157386764 1 1 19 1 gi|14042897|gb|AK027893|AK027893 6170 9520 150 2541 2513 690 27 513 513 517 95 18 100 100 0 1564 1671 570 34 307 307 311 63 20 100 99 0 1.613 1.466 1.558 1.518 1.709 1.410 0.665 156 767 100 3285 3364 0.690 2028 1257 2000 1364 391984 260645 21.011 21.587 0 0 0
237260 1 1 20 1 gi|5901981|ref|NM_006899.1| 6380 9520 140 547 553 104 18 526 526 533 98 18 25 5 0 320 329 78 23 309 309 314 64 20 21 5 0 1.909 1.350 1.319 1.366 4.093 24.361 0.001 156 711 100 32 47 0.933 21 11 27 20 86195 51258 0.204 0.234 -50 0 0

Total number of rows: 15488

Table truncated, full table size 4206 Kbytes.




Supplementary file Size Download File type/resource
GSM252344.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table
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